Mutagenetix > Incidental Mutation

Incidental Mutation 'R4999:Sema6c'

389700

Institutional Source

Beutler Lab

Gene Symbol

Sema6c

Ensembl Gene

ENSMUSG00000038777

Gene Name

sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C

Synonyms

Sema Y, Semay

MMRRC Submission

042593-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.221) question?

Stock #

R4999 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

95067768-95081335 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 95075674 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 175 (T175I)

Ref Sequence

ENSEMBL: ENSMUSP00000144039 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000090821] [ENSMUST00000090823] [ENSMUST00000107217] [ENSMUST00000131620] [ENSMUST00000168321] [ENSMUST00000202315] [ENSMUST00000204709] [ENSMUST00000142449] [ENSMUST00000131742]

AlphaFold

Q9WTM3

Predicted Effect

probably damaging
Transcript: ENSMUST00000090821
AA Change: T175I

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000088331
Gene: ENSMUSG00000038777
AA Change: T175I

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Sema	62	488	2.55e-165	SMART
transmembrane domain	604	626	N/A	INTRINSIC
low complexity region	627	638	N/A	INTRINSIC
low complexity region	646	658	N/A	INTRINSIC
low complexity region	660	669	N/A	INTRINSIC
low complexity region	693	709	N/A	INTRINSIC
low complexity region	744	761	N/A	INTRINSIC
low complexity region	907	924	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000090823
AA Change: T175I

PolyPhen 2 Score 0.955 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000088333
Gene: ENSMUSG00000038777
AA Change: T175I

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Sema	62	488	2.55e-165	SMART
low complexity region	591	603	N/A	INTRINSIC
transmembrane domain	636	658	N/A	INTRINSIC
low complexity region	659	670	N/A	INTRINSIC
low complexity region	678	690	N/A	INTRINSIC
low complexity region	692	701	N/A	INTRINSIC
low complexity region	725	741	N/A	INTRINSIC
low complexity region	776	793	N/A	INTRINSIC
low complexity region	939	956	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000107217
AA Change: T175I

PolyPhen 2 Score 0.786 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000102835
Gene: ENSMUSG00000038777
AA Change: T175I

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Sema	62	448	1.23e-126	SMART
low complexity region	551	563	N/A	INTRINSIC
transmembrane domain	596	618	N/A	INTRINSIC
low complexity region	619	630	N/A	INTRINSIC
low complexity region	638	650	N/A	INTRINSIC
low complexity region	652	661	N/A	INTRINSIC
low complexity region	685	701	N/A	INTRINSIC
low complexity region	736	753	N/A	INTRINSIC
low complexity region	899	916	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126597

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130662

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130814

Predicted Effect

probably benign
Transcript: ENSMUST00000131620

SMART Domains

Protein: ENSMUSP00000138154
Gene: ENSMUSG00000038777

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134125

Predicted Effect

possibly damaging
Transcript: ENSMUST00000168321
AA Change: T175I

PolyPhen 2 Score 0.955 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000129081
Gene: ENSMUSG00000038777
AA Change: T175I

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Sema	62	488	2.55e-165	SMART
transmembrane domain	604	626	N/A	INTRINSIC
low complexity region	627	638	N/A	INTRINSIC
low complexity region	646	658	N/A	INTRINSIC
low complexity region	660	669	N/A	INTRINSIC
low complexity region	693	709	N/A	INTRINSIC
low complexity region	744	761	N/A	INTRINSIC
low complexity region	907	924	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000202315
AA Change: T175I

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000144039
Gene: ENSMUSG00000038777
AA Change: T175I

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Sema	62	488	2.55e-165	SMART
transmembrane domain	604	626	N/A	INTRINSIC
low complexity region	627	638	N/A	INTRINSIC
low complexity region	646	658	N/A	INTRINSIC
low complexity region	660	669	N/A	INTRINSIC
low complexity region	693	709	N/A	INTRINSIC
low complexity region	744	761	N/A	INTRINSIC
low complexity region	907	924	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000142306

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141607

Predicted Effect

probably benign
Transcript: ENSMUST00000204709

SMART Domains

Protein: ENSMUSP00000144702
Gene: ENSMUSG00000038777

Domain	Start	End	E-Value	Type
low complexity region	10	20	N/A	INTRINSIC
PDB:3OKY\|B	25	117	8e-8	PDB
Blast:Sema	62	119	9e-34	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000142449

SMART Domains

Protein: ENSMUSP00000123457
Gene: ENSMUSG00000038777

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Sema	62	488	2.55e-165	SMART
low complexity region	591	603	N/A	INTRINSIC
transmembrane domain	636	658	N/A	INTRINSIC
low complexity region	659	670	N/A	INTRINSIC
low complexity region	678	690	N/A	INTRINSIC
low complexity region	692	701	N/A	INTRINSIC
low complexity region	725	741	N/A	INTRINSIC
low complexity region	776	793	N/A	INTRINSIC
low complexity region	939	956	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000131742

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.4%
20x: 92.7%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the semaphorin family. Semaphorins represent important molecular signals controlling multiple aspects of the cellular response that follows CNS injury, and thus may play an important role in neural regeneration. [provided by RefSeq, May 2010]
PHENOTYPE: Mice homozygous for a targeted mutation display a decrease in pain threshold. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930444P10Rik	A	G	1: 16,139,022 (GRCm39)		probably null	Het
Abca4	T	A	3: 121,899,019 (GRCm39)	V667D	probably damaging	Het
Aco1	A	G	4: 40,176,507 (GRCm39)	I224V	probably damaging	Het
Arel1	C	T	12: 84,978,541 (GRCm39)	V364M	probably damaging	Het
Arhgap42	A	G	9: 9,009,435 (GRCm39)	V484A	probably damaging	Het
Asap2	T	C	12: 21,302,766 (GRCm39)	F681L	probably benign	Het
Atrn	C	A	2: 130,817,874 (GRCm39)	D809E	probably damaging	Het
Ccdc70	G	A	8: 22,463,266 (GRCm39)	V19M	possibly damaging	Het
Ccp110	G	T	7: 118,329,235 (GRCm39)	E73*	probably null	Het
Cfap57	A	C	4: 118,453,045 (GRCm39)	S553A	probably benign	Het
Cftr	A	G	6: 18,221,613 (GRCm39)	K212E	probably benign	Het
Chkb	A	T	15: 89,312,368 (GRCm39)	Y216N	probably damaging	Het
Cntnap2	G	T	6: 45,897,768 (GRCm39)	D149Y	probably damaging	Het
Cpd	A	G	11: 76,737,048 (GRCm39)		probably null	Het
Creb3l1	C	T	2: 91,813,571 (GRCm39)	D489N	probably benign	Het
Crhbp	A	G	13: 95,578,753 (GRCm39)	F123L	probably damaging	Het
Cryab	T	C	9: 50,665,909 (GRCm39)	V100A	possibly damaging	Het
Csmd2	T	C	4: 128,415,723 (GRCm39)	I2684T	probably benign	Het
Ctbp2	G	T	7: 132,616,378 (GRCm39)	P186T	possibly damaging	Het
Ctnna2	T	C	6: 76,892,745 (GRCm39)	N814S	possibly damaging	Het
Dntt	T	C	19: 41,028,295 (GRCm39)	V197A	probably damaging	Het
Fam135a	G	A	1: 24,059,758 (GRCm39)	A1187V	possibly damaging	Het
Filip1l	A	T	16: 57,390,778 (GRCm39)	Q455H	probably benign	Het
Grm2	T	C	9: 106,531,189 (GRCm39)	E100G	probably damaging	Het
Gtf2ird2	G	A	5: 134,246,306 (GRCm39)	V855M	probably damaging	Het
Heatr9	A	T	11: 83,409,618 (GRCm39)	I118N	possibly damaging	Het
Htra3	T	C	5: 35,828,469 (GRCm39)	H137R	probably benign	Het
Iars1	A	G	13: 49,863,137 (GRCm39)	S530G	probably damaging	Het
Klhdc4	T	A	8: 122,523,342 (GRCm39)	M510L	probably benign	Het
Lipc	T	C	9: 70,724,013 (GRCm39)	T204A	probably benign	Het
Lrp1	A	G	10: 127,389,648 (GRCm39)	V3129A	probably damaging	Het
Macf1	G	A	4: 123,388,702 (GRCm39)	T1120I	probably benign	Het
Maco1	A	G	4: 134,555,444 (GRCm39)	I343T	probably benign	Het
Map4	T	C	9: 109,867,445 (GRCm39)		probably benign	Het
Mbtps1	A	T	8: 120,260,087 (GRCm39)	V420D	probably damaging	Het
Mta2	G	T	19: 8,927,747 (GRCm39)	D523Y	probably benign	Het
Mtcl2	C	T	2: 156,864,776 (GRCm39)	G1144D	probably benign	Het
Muc4	A	G	16: 32,576,670 (GRCm39)		probably benign	Het
Mug1	C	T	6: 121,855,902 (GRCm39)	Q965*	probably null	Het
Myo1e	T	A	9: 70,260,594 (GRCm39)	I584N	probably damaging	Het
Nolc1	T	C	19: 46,067,359 (GRCm39)	V80A	probably damaging	Het
Nop56	G	T	2: 130,117,645 (GRCm39)	V91L	probably benign	Het
Or5b99	A	T	19: 12,976,583 (GRCm39)	M78L	probably benign	Het
Or5h23	A	T	16: 58,906,765 (GRCm39)	L27Q	probably damaging	Het
Or6f2	T	C	7: 139,756,933 (GRCm39)	V300A	probably damaging	Het
Osbpl3	T	C	6: 50,313,277 (GRCm39)	E107G	probably damaging	Het
Pde3a	T	A	6: 141,195,751 (GRCm39)	C146S	probably benign	Het
Pfkm	A	G	15: 98,026,123 (GRCm39)	M573V	probably damaging	Het
Pkd1l2	C	T	8: 117,774,113 (GRCm39)		probably null	Het
Plekhg3	T	C	12: 76,612,021 (GRCm39)	I374T	possibly damaging	Het
Ppig	T	A	2: 69,571,830 (GRCm39)	V183D	unknown	Het
Prom1	T	G	5: 44,194,876 (GRCm39)	I290L	probably benign	Het
Rufy3	T	A	5: 88,785,085 (GRCm39)	M387K	probably damaging	Het
Selenoo	G	A	15: 88,978,387 (GRCm39)	R270H	probably damaging	Het
Sema3d	T	A	5: 12,558,054 (GRCm39)		probably null	Het
Serpina3k	T	C	12: 104,307,305 (GRCm39)	I179T	probably damaging	Het
Sf3b3	T	C	8: 111,567,835 (GRCm39)	T207A	probably benign	Het
Slc22a26	C	A	19: 7,779,546 (GRCm39)	R90L	probably damaging	Het
Slitrk5	T	C	14: 111,917,648 (GRCm39)	V424A	probably damaging	Het
Smarca2	G	T	19: 26,698,255 (GRCm39)	E89*	probably null	Het
Stab2	T	A	10: 86,773,773 (GRCm39)	S853C	probably damaging	Het
Stk17b	A	T	1: 53,800,306 (GRCm39)		probably null	Het
Taar5	T	A	10: 23,847,445 (GRCm39)	I281N	possibly damaging	Het
Tars3	A	T	7: 65,308,683 (GRCm39)	E284D	probably damaging	Het
Tbx15	C	A	3: 99,223,649 (GRCm39)	T279K	probably damaging	Het
Tfr2	G	A	5: 137,585,187 (GRCm39)	V740I	probably benign	Het
Tlr12	T	C	4: 128,511,473 (GRCm39)	E259G	probably benign	Het
Tmem145	A	G	7: 25,008,459 (GRCm39)	T302A	probably benign	Het
Trappc14	T	A	5: 138,259,884 (GRCm39)	T391S	probably damaging	Het
Trpa1	G	T	1: 14,946,085 (GRCm39)	H1015Q	probably benign	Het
Tspan8	A	G	10: 115,653,534 (GRCm39)	Y10C	possibly damaging	Het
Ttll7	A	G	3: 146,600,224 (GRCm39)	N44S	probably damaging	Het
Uba7	T	C	9: 107,857,038 (GRCm39)		probably null	Het
Ube2j2	G	A	4: 156,030,841 (GRCm39)	M1I	probably null	Het
Ubr5	C	A	15: 38,009,912 (GRCm39)	A1022S	probably benign	Het
Usf1	T	G	1: 171,243,331 (GRCm39)	I36S	probably damaging	Het
Vmn1r181	A	T	7: 23,683,790 (GRCm39)	D85V	probably damaging	Het
Vmn1r3	A	T	4: 3,185,009 (GRCm39)	Y99*	probably null	Het
Vmn1r72	T	C	7: 11,404,300 (GRCm39)	I49M	possibly damaging	Het
Vmn2r99	A	G	17: 19,582,397 (GRCm39)	M1V	probably null	Het
Vsig10	T	A	5: 117,482,040 (GRCm39)	V410E	probably damaging	Het
Zc3h7b	A	G	15: 81,663,334 (GRCm39)	Y442C	probably damaging	Het
Zfyve26	G	T	12: 79,327,159 (GRCm39)	Y730*	probably null	Het

Other mutations in Sema6c

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01547:Sema6c	APN	3	95,079,709 (GRCm39)	missense	probably damaging	1.00
IGL01631:Sema6c	APN	3	95,077,714 (GRCm39)	missense	probably benign	0.10
IGL01799:Sema6c	APN	3	95,078,142 (GRCm39)	missense	probably damaging	1.00
IGL02237:Sema6c	APN	3	95,077,430 (GRCm39)	missense	probably damaging	1.00
IGL02852:Sema6c	APN	3	95,077,295 (GRCm39)	splice site	probably benign
IGL02874:Sema6c	APN	3	95,077,688 (GRCm39)	missense	probably damaging	1.00
IGL03003:Sema6c	APN	3	95,076,925 (GRCm39)	missense	probably damaging	1.00
BB005:Sema6c	UTSW	3	95,079,620 (GRCm39)	missense	probably damaging	1.00
BB015:Sema6c	UTSW	3	95,079,620 (GRCm39)	missense	probably damaging	1.00
PIT4418001:Sema6c	UTSW	3	95,077,401 (GRCm39)	missense	possibly damaging	0.57
R0558:Sema6c	UTSW	3	95,076,002 (GRCm39)	missense	probably damaging	1.00
R0582:Sema6c	UTSW	3	95,076,508 (GRCm39)	missense	probably damaging	1.00
R0590:Sema6c	UTSW	3	95,079,934 (GRCm39)	missense	probably damaging	1.00
R0685:Sema6c	UTSW	3	95,080,021 (GRCm39)	missense	possibly damaging	0.46
R1056:Sema6c	UTSW	3	95,078,527 (GRCm39)	missense	probably benign	0.15
R1721:Sema6c	UTSW	3	95,078,099 (GRCm39)	missense	probably damaging	0.98
R1867:Sema6c	UTSW	3	95,078,099 (GRCm39)	missense	probably damaging	0.98
R1868:Sema6c	UTSW	3	95,078,124 (GRCm39)	missense	probably damaging	0.99
R2016:Sema6c	UTSW	3	95,078,545 (GRCm39)	missense	probably benign	0.00
R2343:Sema6c	UTSW	3	95,074,394 (GRCm39)	missense	probably damaging	1.00
R2898:Sema6c	UTSW	3	95,080,129 (GRCm39)	missense	probably damaging	1.00
R4095:Sema6c	UTSW	3	95,080,505 (GRCm39)	missense	probably benign	0.03
R5263:Sema6c	UTSW	3	95,080,463 (GRCm39)	missense	probably benign	0.02
R6914:Sema6c	UTSW	3	95,080,519 (GRCm39)	missense	probably benign	0.00
R6942:Sema6c	UTSW	3	95,080,519 (GRCm39)	missense	probably benign	0.00
R7104:Sema6c	UTSW	3	95,076,156 (GRCm39)	missense	possibly damaging	0.95
R7524:Sema6c	UTSW	3	95,074,371 (GRCm39)	missense	probably benign	0.20
R7724:Sema6c	UTSW	3	95,080,510 (GRCm39)	missense	probably damaging	1.00
R7928:Sema6c	UTSW	3	95,079,620 (GRCm39)	missense	probably damaging	1.00
R8045:Sema6c	UTSW	3	95,080,535 (GRCm39)	missense	probably benign	0.27
R8243:Sema6c	UTSW	3	95,079,916 (GRCm39)	missense	probably damaging	1.00
R8790:Sema6c	UTSW	3	95,075,341 (GRCm39)	missense	probably benign	0.34
R9607:Sema6c	UTSW	3	95,076,545 (GRCm39)	missense	probably benign	0.03
R9653:Sema6c	UTSW	3	95,080,525 (GRCm39)	missense	probably benign	0.40
Z1177:Sema6c	UTSW	3	95,075,639 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- AAGCTTTCAGTTTGATGGGAAGAG -3'
(R):5'- TGCAGCTTGTCTCCTACTGG -3'

Sequencing Primer
(F):5'- TTTGATGGGAAGAGATGGGCATC -3'
(R):5'- GGTGTACACAGATATCTACCTAGGC -3'

Posted On

2016-06-06